verbose      = 2
CodonFreq    = 2
ncatG        = 10
cleandata    = 0
fix_blength  = 0
NSsites      = 1
fix_omega    = 0
clock        = 0
seqfile      = algn
runmode      = 0
fix_kappa    = 0
Small_Diff   = .5e-6
aaDist       = 0
RateAncestor = 0
outfile      = M1.out
icode        = 0
seqtype      = 1
omega        = 1.3
getSE        = 0
noisy        = 0
Mgene        = 0
kappa        = 0.3
treefile     = tree
model        = 0
